Data from: Geneious! Simplified genome skimming methods for phylogenetic systematic studies: a case study in Oreocarya (Boraginaceae)

Premise of the study: As systematists grapple with how to best harness the power of next-generation sequencing (NGS), a deluge of review papers, methods, and analytical tools make choosing the right method difficult. Oreocarya (Boraginaceae), a genus of 63 species, is a good example of a group lacking both species-level resolution and genomic resources. The use of Geneious removes bioinformatic barriers and makes NGS genome skimming accessible to even the least tech-savvy systematists. Methods: A combination of de novo and reference-guided assemblies was used to process 100-bp single-end Illumina HiSeq 2000 reads. A subset of 25 taxa was used to test the suitability of genome skimming for future systematic studies in recalcitrant lineages like Oreocarya. Results: The nuclear ribosomal cistron, the plastome, and 12 mitochondrial genes were recovered from all 25 taxa. All data processing and phylogenomic analyses were performed in Geneious. We report possible future multiplexing levels and published low-copy nuclear genes represented within de novo contigs. Discussion: Genome skimming represents a much-improved primary data collection over PCR+Sanger sequencing when chloroplast DNA (cpDNA), nuclear ribosomal DNA (nrDNA), and mitochondrial DNA (mtDNA) are the target sequences. This study details methods that plant systematists can employ to study their own taxa of interest.

研究背景：当系统分类学家致力于充分发挥新一代测序（next-generation sequencing, NGS）技术的效能时，海量的综述文献、实验方法与分析工具层出不穷，导致研究者难以遴选适配的研究方案。紫草科（Boraginaceae）厚壳草属（Oreocarya）包含63个物种，该类群便是既缺乏物种水平分辨率、又存在基因组资源匮乏问题的典型代表。Geneious软件可破除生物信息学技术壁垒，即便是对生物信息学操作较为生疏的系统分类学家，也能够轻松开展NGS基因组浅层测序工作。

研究方法：本研究采用从头组装与参考基因组引导组装相结合的策略，对100 bp单端Illumina HiSeq 2000测序读段进行数据处理。选取25个分类群作为测试子集，用以验证基因组浅层测序在厚壳草属这类疑难演化支的后续系统学研究中的适用性。

研究结果：从全部25个分类群中均成功获取了核核糖体基因簇、质体基因组以及12个线粒体基因的序列数据。所有数据处理与系统发育基因组学分析均在Geneious软件中完成。本研究还报道了潜在的未来多重测序通量水平，以及从头组装重叠群中包含的已发表低拷贝核基因信息。

研究讨论：当以叶绿体DNA（chloroplast DNA, cpDNA）、核核糖体DNA（nuclear ribosomal DNA, nrDNA）与线粒体DNA（mitochondrial DNA, mtDNA）为靶标序列时，基因组浅层测序相较于传统的PCR+桑格测序，是更为高效优质的基础数据获取手段。本研究详细阐述了植物系统分类学家可用于开展自身目标类群研究的具体实验方法。